Starting phenix.real_space_refine on Thu Feb 5 12:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hey_52101/02_2026/9hey_52101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hey_52101/02_2026/9hey_52101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hey_52101/02_2026/9hey_52101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hey_52101/02_2026/9hey_52101.map" model { file = "/net/cci-nas-00/data/ceres_data/9hey_52101/02_2026/9hey_52101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hey_52101/02_2026/9hey_52101.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 11375 2.51 5 N 2604 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17038 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2434 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.13, per 1000 atoms: 0.13 Number of scatterers: 17038 At special positions: 0 Unit cell: (112.2, 110.55, 117.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2968 8.00 N 2604 7.00 C 11375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 264 " distance=2.02 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.02 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.02 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.02 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.02 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.02 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 751.2 milliseconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4130 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 75.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 131 removed outlier: 3.590A pdb=" N TRP A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.719A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 268 through 294 Proline residue: A 288 - end of helix removed outlier: 3.685A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.632A pdb=" N TYR A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.676A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 131 removed outlier: 3.589A pdb=" N TRP B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 155 removed outlier: 4.718A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 140 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 268 through 294 Proline residue: B 288 - end of helix removed outlier: 3.686A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.632A pdb=" N TYR B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.677A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 131 removed outlier: 3.590A pdb=" N TRP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 155 removed outlier: 4.719A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 140 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 268 through 294 Proline residue: C 288 - end of helix removed outlier: 3.685A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 304 through 310 removed outlier: 3.632A pdb=" N TYR C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.676A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 131 removed outlier: 3.590A pdb=" N TRP D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 155 removed outlier: 4.719A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 140 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 268 through 294 Proline residue: D 288 - end of helix removed outlier: 3.685A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 304 through 310 removed outlier: 3.632A pdb=" N TYR D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.676A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 131 removed outlier: 3.590A pdb=" N TRP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 155 removed outlier: 4.719A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 140 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'E' and resid 268 through 294 Proline residue: E 288 - end of helix removed outlier: 3.685A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 304 through 310 removed outlier: 3.632A pdb=" N TYR E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.676A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 131 removed outlier: 3.589A pdb=" N TRP F 104 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 155 removed outlier: 4.719A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 140 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 203 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 268 through 294 Proline residue: F 288 - end of helix removed outlier: 3.686A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 304 through 310 removed outlier: 3.633A pdb=" N TYR F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.677A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 355 Processing helix chain 'F' and resid 362 through 369 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 131 removed outlier: 3.589A pdb=" N TRP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 155 removed outlier: 4.719A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 140 " --> pdb=" O CYS G 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 203 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 268 through 294 Proline residue: G 288 - end of helix removed outlier: 3.686A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 304 through 310 removed outlier: 3.633A pdb=" N TYR G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.676A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 355 Processing helix chain 'G' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.543A pdb=" N LEU A 244 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.544A pdb=" N LEU B 244 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.543A pdb=" N LEU C 244 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.543A pdb=" N LEU D 244 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.544A pdb=" N LEU E 244 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.544A pdb=" N LEU F 244 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.543A pdb=" N LEU G 244 " --> pdb=" O GLN G 95 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4991 1.34 - 1.46: 3723 1.46 - 1.57: 8611 1.57 - 1.69: 0 1.69 - 1.81: 119 Bond restraints: 17444 Sorted by residual: bond pdb=" CA ASN G 204 " pdb=" C ASN G 204 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.12e-02 7.97e+03 1.09e+00 bond pdb=" CA ASN B 204 " pdb=" C ASN B 204 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.12e-02 7.97e+03 1.08e+00 bond pdb=" C ALA C 53 " pdb=" N PHE C 54 " ideal model delta sigma weight residual 1.333 1.321 0.013 1.24e-02 6.50e+03 1.06e+00 bond pdb=" CA ASN F 204 " pdb=" C ASN F 204 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.12e-02 7.97e+03 1.05e+00 bond pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta sigma weight residual 1.463 1.452 0.011 1.08e-02 8.57e+03 1.05e+00 ... (remaining 17439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 21930 1.21 - 2.41: 1345 2.41 - 3.62: 210 3.62 - 4.82: 113 4.82 - 6.03: 62 Bond angle restraints: 23660 Sorted by residual: angle pdb=" C ALA A 55 " pdb=" N GLN A 56 " pdb=" CA GLN A 56 " ideal model delta sigma weight residual 120.88 116.97 3.91 1.62e+00 3.81e-01 5.83e+00 angle pdb=" C ALA E 55 " pdb=" N GLN E 56 " pdb=" CA GLN E 56 " ideal model delta sigma weight residual 120.88 117.00 3.88 1.62e+00 3.81e-01 5.72e+00 angle pdb=" C ALA G 55 " pdb=" N GLN G 56 " pdb=" CA GLN G 56 " ideal model delta sigma weight residual 120.88 117.01 3.87 1.62e+00 3.81e-01 5.71e+00 angle pdb=" C ALA B 55 " pdb=" N GLN B 56 " pdb=" CA GLN B 56 " ideal model delta sigma weight residual 120.88 117.01 3.87 1.62e+00 3.81e-01 5.70e+00 angle pdb=" C ALA D 55 " pdb=" N GLN D 56 " pdb=" CA GLN D 56 " ideal model delta sigma weight residual 120.88 117.03 3.85 1.62e+00 3.81e-01 5.65e+00 ... (remaining 23655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 9681 16.67 - 33.34: 644 33.34 - 50.01: 84 50.01 - 66.69: 35 66.69 - 83.36: 14 Dihedral angle restraints: 10458 sinusoidal: 4123 harmonic: 6335 Sorted by residual: dihedral pdb=" CA GLN D 90 " pdb=" C GLN D 90 " pdb=" N LYS D 91 " pdb=" CA LYS D 91 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLN C 90 " pdb=" C GLN C 90 " pdb=" N LYS C 91 " pdb=" CA LYS C 91 " ideal model delta harmonic sigma weight residual 180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLN B 90 " pdb=" C GLN B 90 " pdb=" N LYS B 91 " pdb=" CA LYS B 91 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 10455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1928 0.041 - 0.083: 739 0.083 - 0.124: 132 0.124 - 0.166: 8 0.166 - 0.207: 7 Chirality restraints: 2814 Sorted by residual: chirality pdb=" CA GLU A 57 " pdb=" N GLU A 57 " pdb=" C GLU A 57 " pdb=" CB GLU A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA GLU E 57 " pdb=" N GLU E 57 " pdb=" C GLU E 57 " pdb=" CB GLU E 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU F 57 " pdb=" N GLU F 57 " pdb=" C GLU F 57 " pdb=" CB GLU F 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2811 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 58 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C ILE E 58 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE E 58 " 0.009 2.00e-02 2.50e+03 pdb=" N SER E 59 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 58 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C ILE B 58 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 58 " 0.009 2.00e-02 2.50e+03 pdb=" N SER B 59 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 58 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ILE G 58 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE G 58 " 0.009 2.00e-02 2.50e+03 pdb=" N SER G 59 " 0.008 2.00e-02 2.50e+03 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4244 2.79 - 3.32: 18580 3.32 - 3.84: 28162 3.84 - 4.37: 34035 4.37 - 4.90: 55189 Nonbonded interactions: 140210 Sorted by model distance: nonbonded pdb=" O ASN A 352 " pdb=" OG SER A 355 " model vdw 2.259 3.040 nonbonded pdb=" O ASN E 352 " pdb=" OG SER E 355 " model vdw 2.259 3.040 nonbonded pdb=" O ASN G 352 " pdb=" OG SER G 355 " model vdw 2.259 3.040 nonbonded pdb=" O ASN B 352 " pdb=" OG SER B 355 " model vdw 2.259 3.040 nonbonded pdb=" O ASN D 352 " pdb=" OG SER D 355 " model vdw 2.260 3.040 ... (remaining 140205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 14.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17458 Z= 0.261 Angle : 0.759 6.027 23688 Z= 0.401 Chirality : 0.043 0.207 2814 Planarity : 0.005 0.049 2828 Dihedral : 12.039 83.357 6286 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.39 % Favored : 95.27 % Rotamer: Outliers : 0.36 % Allowed : 1.44 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2072 helix: -1.03 (0.12), residues: 1414 sheet: None (None), residues: 0 loop : -0.83 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG E 216 TYR 0.015 0.004 TYR G 150 PHE 0.017 0.002 PHE G 126 TRP 0.013 0.002 TRP C 127 HIS 0.007 0.002 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00567 (17444) covalent geometry : angle 0.75791 (23660) SS BOND : bond 0.00605 ( 14) SS BOND : angle 1.58309 ( 28) hydrogen bonds : bond 0.20563 ( 1113) hydrogen bonds : angle 7.53683 ( 3087) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 640 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8705 (m-30) cc_final: 0.8396 (t0) REVERT: A 48 LEU cc_start: 0.9632 (tp) cc_final: 0.9405 (tp) REVERT: A 135 LEU cc_start: 0.9422 (tp) cc_final: 0.9066 (pp) REVERT: A 255 ASP cc_start: 0.8958 (t0) cc_final: 0.8725 (t0) REVERT: A 258 ILE cc_start: 0.9414 (mt) cc_final: 0.9209 (mt) REVERT: A 303 ASP cc_start: 0.8573 (m-30) cc_final: 0.8319 (t0) REVERT: A 332 LEU cc_start: 0.9834 (mp) cc_final: 0.9618 (mm) REVERT: B 35 ASP cc_start: 0.8648 (m-30) cc_final: 0.8362 (t0) REVERT: B 128 ARG cc_start: 0.9306 (ttt180) cc_final: 0.8982 (tpt90) REVERT: B 285 LEU cc_start: 0.9074 (mt) cc_final: 0.8848 (tt) REVERT: B 303 ASP cc_start: 0.8469 (m-30) cc_final: 0.8254 (t0) REVERT: B 332 LEU cc_start: 0.9826 (mp) cc_final: 0.9511 (mm) REVERT: C 128 ARG cc_start: 0.9307 (ttt180) cc_final: 0.8987 (ttp-110) REVERT: C 285 LEU cc_start: 0.9098 (mt) cc_final: 0.8821 (tt) REVERT: C 303 ASP cc_start: 0.8590 (m-30) cc_final: 0.8335 (t0) REVERT: C 332 LEU cc_start: 0.9835 (mp) cc_final: 0.9537 (mm) REVERT: D 135 LEU cc_start: 0.9421 (tp) cc_final: 0.9082 (pp) REVERT: D 285 LEU cc_start: 0.9093 (mt) cc_final: 0.8823 (tt) REVERT: D 303 ASP cc_start: 0.8421 (m-30) cc_final: 0.8180 (t0) REVERT: D 332 LEU cc_start: 0.9823 (mp) cc_final: 0.9529 (mm) REVERT: E 128 ARG cc_start: 0.9323 (ttt180) cc_final: 0.9031 (tpt90) REVERT: E 285 LEU cc_start: 0.9069 (mt) cc_final: 0.8855 (tt) REVERT: E 303 ASP cc_start: 0.8543 (m-30) cc_final: 0.8320 (t0) REVERT: E 332 LEU cc_start: 0.9828 (mp) cc_final: 0.9513 (mm) REVERT: F 285 LEU cc_start: 0.9121 (mt) cc_final: 0.8856 (tt) REVERT: F 303 ASP cc_start: 0.8574 (m-30) cc_final: 0.8337 (t0) REVERT: F 332 LEU cc_start: 0.9826 (mp) cc_final: 0.9514 (mm) REVERT: G 128 ARG cc_start: 0.9320 (ttt180) cc_final: 0.9080 (tpt90) REVERT: G 285 LEU cc_start: 0.9021 (mt) cc_final: 0.8792 (tt) REVERT: G 332 LEU cc_start: 0.9830 (mp) cc_final: 0.9533 (mm) outliers start: 7 outliers final: 0 residues processed: 640 average time/residue: 0.1255 time to fit residues: 118.5618 Evaluate side-chains 405 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN D 352 ASN E 318 HIS F 318 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.057539 restraints weight = 72373.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059512 restraints weight = 41607.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060868 restraints weight = 28095.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061764 restraints weight = 21176.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062375 restraints weight = 17360.620| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17458 Z= 0.153 Angle : 0.746 10.502 23688 Z= 0.365 Chirality : 0.042 0.151 2814 Planarity : 0.004 0.027 2828 Dihedral : 5.405 17.255 2247 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.61 % Allowed : 11.14 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2072 helix: 0.89 (0.13), residues: 1386 sheet: -1.39 (0.62), residues: 70 loop : -0.34 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 152 TYR 0.018 0.001 TYR D 150 PHE 0.033 0.002 PHE B 314 TRP 0.007 0.001 TRP A 104 HIS 0.002 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00332 (17444) covalent geometry : angle 0.74505 (23660) SS BOND : bond 0.00230 ( 14) SS BOND : angle 1.15051 ( 28) hydrogen bonds : bond 0.04346 ( 1113) hydrogen bonds : angle 4.86116 ( 3087) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 470 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8976 (m-30) cc_final: 0.8672 (t70) REVERT: A 37 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8241 (ppp) REVERT: A 135 LEU cc_start: 0.9386 (tp) cc_final: 0.9037 (pp) REVERT: A 255 ASP cc_start: 0.9010 (t0) cc_final: 0.8682 (t0) REVERT: A 258 ILE cc_start: 0.9478 (mt) cc_final: 0.9256 (mt) REVERT: A 334 LEU cc_start: 0.9506 (mt) cc_final: 0.9248 (pp) REVERT: B 35 ASP cc_start: 0.8972 (m-30) cc_final: 0.8639 (t70) REVERT: B 146 LEU cc_start: 0.9754 (mt) cc_final: 0.9434 (pp) REVERT: B 334 LEU cc_start: 0.9483 (mt) cc_final: 0.9207 (pp) REVERT: C 128 ARG cc_start: 0.9312 (ttt180) cc_final: 0.9013 (ttp-110) REVERT: C 334 LEU cc_start: 0.9508 (mt) cc_final: 0.9271 (pp) REVERT: C 363 MET cc_start: 0.7355 (pmm) cc_final: 0.7129 (pmm) REVERT: D 135 LEU cc_start: 0.9382 (tp) cc_final: 0.9039 (pp) REVERT: D 334 LEU cc_start: 0.9481 (mt) cc_final: 0.9219 (pp) REVERT: D 363 MET cc_start: 0.7466 (pmm) cc_final: 0.6996 (pmm) REVERT: E 37 MET cc_start: 0.8785 (ttt) cc_final: 0.8278 (ppp) REVERT: E 334 LEU cc_start: 0.9488 (mt) cc_final: 0.9195 (pp) REVERT: F 135 LEU cc_start: 0.9459 (tp) cc_final: 0.9053 (pp) REVERT: F 285 LEU cc_start: 0.9035 (mt) cc_final: 0.8813 (tt) REVERT: F 334 LEU cc_start: 0.9452 (mt) cc_final: 0.9148 (pp) REVERT: G 334 LEU cc_start: 0.9478 (mt) cc_final: 0.9226 (pp) outliers start: 70 outliers final: 43 residues processed: 507 average time/residue: 0.1231 time to fit residues: 94.8504 Evaluate side-chains 416 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 279 ASN C 279 ASN D 100 ASN D 279 ASN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 279 ASN G 100 ASN G 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.074526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057146 restraints weight = 70753.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059093 restraints weight = 41076.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060428 restraints weight = 27814.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.061059 restraints weight = 21389.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061749 restraints weight = 18256.898| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17458 Z= 0.123 Angle : 0.699 11.522 23688 Z= 0.335 Chirality : 0.041 0.190 2814 Planarity : 0.003 0.026 2828 Dihedral : 4.872 16.872 2247 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.78 % Allowed : 15.99 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 2072 helix: 1.16 (0.14), residues: 1435 sheet: -0.88 (0.63), residues: 70 loop : 0.32 (0.30), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 152 TYR 0.015 0.001 TYR E 150 PHE 0.025 0.001 PHE B 314 TRP 0.003 0.001 TRP E 74 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00264 (17444) covalent geometry : angle 0.69892 (23660) SS BOND : bond 0.00090 ( 14) SS BOND : angle 0.90430 ( 28) hydrogen bonds : bond 0.03750 ( 1113) hydrogen bonds : angle 4.47913 ( 3087) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8959 (m-30) cc_final: 0.8720 (t70) REVERT: A 37 MET cc_start: 0.8717 (ttt) cc_final: 0.8281 (ppp) REVERT: A 56 GLN cc_start: 0.7748 (tp40) cc_final: 0.6994 (tp-100) REVERT: A 63 GLN cc_start: 0.8641 (mp10) cc_final: 0.8420 (mp10) REVERT: A 135 LEU cc_start: 0.9401 (tp) cc_final: 0.9088 (pp) REVERT: A 146 LEU cc_start: 0.9710 (mt) cc_final: 0.9334 (pp) REVERT: A 255 ASP cc_start: 0.9051 (t0) cc_final: 0.8805 (t0) REVERT: A 309 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9173 (tp30) REVERT: A 334 LEU cc_start: 0.9585 (mt) cc_final: 0.9318 (pp) REVERT: A 336 GLU cc_start: 0.9548 (tp30) cc_final: 0.9206 (tp30) REVERT: B 35 ASP cc_start: 0.8968 (m-30) cc_final: 0.8579 (t70) REVERT: B 37 MET cc_start: 0.8818 (ttt) cc_final: 0.8307 (ppp) REVERT: B 56 GLN cc_start: 0.7689 (tp40) cc_final: 0.7286 (tp-100) REVERT: B 134 HIS cc_start: 0.9043 (t70) cc_final: 0.8823 (t70) REVERT: B 260 ASP cc_start: 0.9194 (p0) cc_final: 0.8750 (p0) REVERT: B 261 ARG cc_start: 0.8739 (mmt-90) cc_final: 0.8519 (tpp-160) REVERT: B 309 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9038 (tp30) REVERT: B 334 LEU cc_start: 0.9553 (mt) cc_final: 0.9269 (pp) REVERT: B 336 GLU cc_start: 0.9551 (tp30) cc_final: 0.9220 (tp30) REVERT: C 37 MET cc_start: 0.8823 (ttt) cc_final: 0.8330 (ppp) REVERT: C 56 GLN cc_start: 0.7602 (tp40) cc_final: 0.7229 (tp-100) REVERT: C 128 ARG cc_start: 0.9260 (ttt180) cc_final: 0.8985 (ttp-110) REVERT: C 134 HIS cc_start: 0.9010 (t70) cc_final: 0.8725 (t70) REVERT: C 334 LEU cc_start: 0.9575 (mt) cc_final: 0.9314 (pp) REVERT: C 336 GLU cc_start: 0.9531 (tp30) cc_final: 0.9206 (tp30) REVERT: C 363 MET cc_start: 0.7386 (pmm) cc_final: 0.7090 (pmm) REVERT: D 37 MET cc_start: 0.8816 (ttt) cc_final: 0.8355 (ppp) REVERT: D 56 GLN cc_start: 0.7683 (tp40) cc_final: 0.7260 (tp-100) REVERT: D 109 PHE cc_start: 0.9144 (t80) cc_final: 0.8700 (t80) REVERT: D 134 HIS cc_start: 0.9018 (t70) cc_final: 0.8768 (t-170) REVERT: D 135 LEU cc_start: 0.9351 (tp) cc_final: 0.8974 (pp) REVERT: D 260 ASP cc_start: 0.9214 (p0) cc_final: 0.8843 (p0) REVERT: D 309 GLU cc_start: 0.9381 (tm-30) cc_final: 0.9024 (tp30) REVERT: D 334 LEU cc_start: 0.9535 (mt) cc_final: 0.9290 (pp) REVERT: D 336 GLU cc_start: 0.9565 (tp30) cc_final: 0.9220 (tp30) REVERT: E 37 MET cc_start: 0.8767 (ttt) cc_final: 0.8327 (ppp) REVERT: E 56 GLN cc_start: 0.7776 (tp40) cc_final: 0.7296 (tp-100) REVERT: E 134 HIS cc_start: 0.9103 (t70) cc_final: 0.8891 (t70) REVERT: E 143 MET cc_start: 0.8724 (ttt) cc_final: 0.8146 (tmm) REVERT: E 279 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8529 (m110) REVERT: E 334 LEU cc_start: 0.9533 (mt) cc_final: 0.9260 (pp) REVERT: E 336 GLU cc_start: 0.9539 (tp30) cc_final: 0.9205 (tp30) REVERT: F 37 MET cc_start: 0.8787 (ttt) cc_final: 0.8327 (ppp) REVERT: F 56 GLN cc_start: 0.7783 (tp40) cc_final: 0.7339 (tp-100) REVERT: F 134 HIS cc_start: 0.9073 (t70) cc_final: 0.8869 (t70) REVERT: F 135 LEU cc_start: 0.9450 (tp) cc_final: 0.9062 (pp) REVERT: F 146 LEU cc_start: 0.9733 (mt) cc_final: 0.9370 (pp) REVERT: F 334 LEU cc_start: 0.9502 (mt) cc_final: 0.9222 (pp) REVERT: F 336 GLU cc_start: 0.9572 (tp30) cc_final: 0.9258 (tp30) REVERT: G 37 MET cc_start: 0.8733 (ttt) cc_final: 0.8295 (ppp) REVERT: G 54 PHE cc_start: 0.9076 (m-80) cc_final: 0.8524 (t80) REVERT: G 56 GLN cc_start: 0.7718 (tp40) cc_final: 0.7299 (tp-100) REVERT: G 134 HIS cc_start: 0.9125 (t70) cc_final: 0.8779 (t70) REVERT: G 146 LEU cc_start: 0.9727 (mt) cc_final: 0.9347 (pp) REVERT: G 334 LEU cc_start: 0.9565 (mt) cc_final: 0.9309 (pp) REVERT: G 336 GLU cc_start: 0.9545 (tp30) cc_final: 0.9204 (tp30) REVERT: G 363 MET cc_start: 0.7266 (pmm) cc_final: 0.7001 (pmm) outliers start: 54 outliers final: 26 residues processed: 470 average time/residue: 0.1361 time to fit residues: 97.3811 Evaluate side-chains 413 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 386 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 352 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.076383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059671 restraints weight = 71673.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061601 restraints weight = 41707.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062947 restraints weight = 28337.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063882 restraints weight = 21288.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064515 restraints weight = 17345.507| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17458 Z= 0.117 Angle : 0.677 8.786 23688 Z= 0.322 Chirality : 0.041 0.274 2814 Planarity : 0.003 0.026 2828 Dihedral : 4.614 16.518 2247 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.76 % Allowed : 16.14 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2072 helix: 1.33 (0.14), residues: 1428 sheet: -0.63 (0.63), residues: 70 loop : 0.46 (0.30), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 261 TYR 0.025 0.001 TYR A 121 PHE 0.027 0.001 PHE G 314 TRP 0.003 0.001 TRP E 74 HIS 0.006 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00246 (17444) covalent geometry : angle 0.67657 (23660) SS BOND : bond 0.00093 ( 14) SS BOND : angle 0.76619 ( 28) hydrogen bonds : bond 0.03504 ( 1113) hydrogen bonds : angle 4.31497 ( 3087) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 435 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8901 (m-30) cc_final: 0.8672 (t70) REVERT: A 37 MET cc_start: 0.8714 (ttt) cc_final: 0.8292 (ppp) REVERT: A 56 GLN cc_start: 0.7721 (tp40) cc_final: 0.7344 (tp-100) REVERT: A 63 GLN cc_start: 0.8644 (mp10) cc_final: 0.8440 (mp10) REVERT: A 109 PHE cc_start: 0.9096 (t80) cc_final: 0.8840 (t80) REVERT: A 135 LEU cc_start: 0.9339 (tp) cc_final: 0.9037 (pp) REVERT: A 309 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9190 (tp30) REVERT: A 334 LEU cc_start: 0.9608 (mt) cc_final: 0.9344 (pp) REVERT: A 336 GLU cc_start: 0.9535 (tp30) cc_final: 0.9275 (tm-30) REVERT: B 35 ASP cc_start: 0.8960 (m-30) cc_final: 0.8612 (t70) REVERT: B 37 MET cc_start: 0.8761 (ttt) cc_final: 0.8304 (ppp) REVERT: B 56 GLN cc_start: 0.7719 (tp40) cc_final: 0.7359 (tp-100) REVERT: B 109 PHE cc_start: 0.9172 (t80) cc_final: 0.8514 (t80) REVERT: B 134 HIS cc_start: 0.8999 (t70) cc_final: 0.8776 (t-170) REVERT: B 152 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8787 (mmp80) REVERT: B 334 LEU cc_start: 0.9553 (mt) cc_final: 0.9311 (pp) REVERT: B 336 GLU cc_start: 0.9552 (tp30) cc_final: 0.9300 (tm-30) REVERT: B 363 MET cc_start: 0.7042 (pmm) cc_final: 0.6791 (pmm) REVERT: C 37 MET cc_start: 0.8820 (ttt) cc_final: 0.8344 (ppp) REVERT: C 56 GLN cc_start: 0.7626 (tp40) cc_final: 0.7306 (tp-100) REVERT: C 109 PHE cc_start: 0.9118 (t80) cc_final: 0.8555 (t80) REVERT: C 128 ARG cc_start: 0.9239 (ttt180) cc_final: 0.9019 (ttp-110) REVERT: C 134 HIS cc_start: 0.9001 (t70) cc_final: 0.8753 (t-170) REVERT: C 309 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9156 (tp30) REVERT: C 334 LEU cc_start: 0.9594 (mt) cc_final: 0.9354 (pp) REVERT: C 336 GLU cc_start: 0.9521 (tp30) cc_final: 0.9273 (tm-30) REVERT: C 363 MET cc_start: 0.7804 (pmm) cc_final: 0.7532 (pmm) REVERT: D 37 MET cc_start: 0.8805 (ttt) cc_final: 0.8387 (ppp) REVERT: D 56 GLN cc_start: 0.7790 (tp40) cc_final: 0.7407 (tp-100) REVERT: D 109 PHE cc_start: 0.9111 (t80) cc_final: 0.8591 (t80) REVERT: D 135 LEU cc_start: 0.9406 (tp) cc_final: 0.8953 (pp) REVERT: D 309 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9143 (tp30) REVERT: D 334 LEU cc_start: 0.9553 (mt) cc_final: 0.9307 (pp) REVERT: D 336 GLU cc_start: 0.9546 (tp30) cc_final: 0.9284 (tm-30) REVERT: E 37 MET cc_start: 0.8819 (ttt) cc_final: 0.8341 (ppp) REVERT: E 56 GLN cc_start: 0.7779 (tp40) cc_final: 0.7375 (tp-100) REVERT: E 109 PHE cc_start: 0.9079 (t80) cc_final: 0.8509 (t80) REVERT: E 134 HIS cc_start: 0.8985 (t70) cc_final: 0.8696 (t-170) REVERT: E 334 LEU cc_start: 0.9560 (mt) cc_final: 0.9321 (pp) REVERT: E 336 GLU cc_start: 0.9543 (tp30) cc_final: 0.9269 (tm-30) REVERT: E 346 CYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9251 (p) REVERT: E 347 LEU cc_start: 0.9771 (mt) cc_final: 0.9485 (mt) REVERT: F 37 MET cc_start: 0.8778 (ttt) cc_final: 0.8341 (ppp) REVERT: F 56 GLN cc_start: 0.7808 (tp40) cc_final: 0.7420 (tp-100) REVERT: F 109 PHE cc_start: 0.9127 (t80) cc_final: 0.8897 (t80) REVERT: F 134 HIS cc_start: 0.8998 (t70) cc_final: 0.8758 (t-170) REVERT: F 309 GLU cc_start: 0.9353 (tm-30) cc_final: 0.9140 (tp30) REVERT: F 334 LEU cc_start: 0.9516 (mt) cc_final: 0.9275 (pp) REVERT: F 336 GLU cc_start: 0.9569 (tp30) cc_final: 0.9296 (tm-30) REVERT: G 37 MET cc_start: 0.8749 (ttt) cc_final: 0.8306 (ppp) REVERT: G 56 GLN cc_start: 0.7789 (tp40) cc_final: 0.7404 (tp-100) REVERT: G 63 GLN cc_start: 0.8513 (mp10) cc_final: 0.8304 (mp10) REVERT: G 109 PHE cc_start: 0.9171 (t80) cc_final: 0.8865 (t80) REVERT: G 134 HIS cc_start: 0.9039 (t70) cc_final: 0.8815 (t-170) REVERT: G 146 LEU cc_start: 0.9735 (mt) cc_final: 0.9407 (pp) REVERT: G 309 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9174 (tp30) REVERT: G 334 LEU cc_start: 0.9580 (mt) cc_final: 0.9350 (pp) REVERT: G 336 GLU cc_start: 0.9538 (tp30) cc_final: 0.9261 (tm-30) REVERT: G 363 MET cc_start: 0.7475 (pmm) cc_final: 0.7115 (pmm) outliers start: 73 outliers final: 45 residues processed: 483 average time/residue: 0.1317 time to fit residues: 96.6701 Evaluate side-chains 422 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 376 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 303 ASP Chi-restraints excluded: chain G residue 346 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 0.3980 chunk 191 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 100 ASN A 134 HIS C 318 HIS D 134 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 352 ASN G 100 ASN G 318 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.074327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.057518 restraints weight = 73047.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059341 restraints weight = 42957.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060628 restraints weight = 29646.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.061484 restraints weight = 22603.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.062067 restraints weight = 18661.076| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17458 Z= 0.154 Angle : 0.700 11.832 23688 Z= 0.337 Chirality : 0.042 0.246 2814 Planarity : 0.003 0.023 2828 Dihedral : 4.670 17.615 2247 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.59 % Allowed : 18.21 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 2072 helix: 1.11 (0.14), residues: 1470 sheet: -0.72 (0.63), residues: 70 loop : 0.13 (0.32), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 152 TYR 0.023 0.001 TYR A 121 PHE 0.016 0.001 PHE A 319 TRP 0.004 0.001 TRP A 74 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00340 (17444) covalent geometry : angle 0.69997 (23660) SS BOND : bond 0.00265 ( 14) SS BOND : angle 0.97192 ( 28) hydrogen bonds : bond 0.03538 ( 1113) hydrogen bonds : angle 4.48668 ( 3087) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 402 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8945 (m-30) cc_final: 0.8728 (t70) REVERT: A 37 MET cc_start: 0.8746 (ttt) cc_final: 0.8342 (ppp) REVERT: A 56 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7493 (tp-100) REVERT: A 63 GLN cc_start: 0.8689 (mp10) cc_final: 0.8451 (mp10) REVERT: A 109 PHE cc_start: 0.9178 (t80) cc_final: 0.8916 (t80) REVERT: A 135 LEU cc_start: 0.9423 (tp) cc_final: 0.9050 (pp) REVERT: A 309 GLU cc_start: 0.9442 (tm-30) cc_final: 0.9216 (tp30) REVERT: A 334 LEU cc_start: 0.9642 (mt) cc_final: 0.9407 (pp) REVERT: A 336 GLU cc_start: 0.9558 (tp30) cc_final: 0.9255 (tm-30) REVERT: B 35 ASP cc_start: 0.8993 (m-30) cc_final: 0.8685 (t70) REVERT: B 37 MET cc_start: 0.8772 (ttt) cc_final: 0.8345 (ppp) REVERT: B 56 GLN cc_start: 0.7939 (tp40) cc_final: 0.7590 (tp-100) REVERT: B 109 PHE cc_start: 0.9195 (t80) cc_final: 0.8630 (t80) REVERT: B 113 LEU cc_start: 0.9583 (tp) cc_final: 0.9374 (tp) REVERT: B 135 LEU cc_start: 0.9483 (tp) cc_final: 0.9080 (pp) REVERT: B 146 LEU cc_start: 0.9735 (mt) cc_final: 0.9366 (pp) REVERT: B 309 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9118 (tp30) REVERT: B 334 LEU cc_start: 0.9599 (mt) cc_final: 0.9351 (pp) REVERT: B 336 GLU cc_start: 0.9586 (tp30) cc_final: 0.9298 (tm-30) REVERT: B 363 MET cc_start: 0.7284 (pmm) cc_final: 0.6994 (pmm) REVERT: C 37 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8400 (ppp) REVERT: C 56 GLN cc_start: 0.7837 (tp40) cc_final: 0.7512 (tp-100) REVERT: C 109 PHE cc_start: 0.9208 (t80) cc_final: 0.8683 (t80) REVERT: C 134 HIS cc_start: 0.9011 (t70) cc_final: 0.8789 (t70) REVERT: C 334 LEU cc_start: 0.9611 (mt) cc_final: 0.9359 (pp) REVERT: C 336 GLU cc_start: 0.9556 (tp30) cc_final: 0.9263 (tm-30) REVERT: C 363 MET cc_start: 0.7784 (pmm) cc_final: 0.7497 (pmm) REVERT: D 37 MET cc_start: 0.8842 (ttt) cc_final: 0.8478 (ppp) REVERT: D 56 GLN cc_start: 0.7893 (tp40) cc_final: 0.7530 (tp-100) REVERT: D 109 PHE cc_start: 0.9201 (t80) cc_final: 0.8715 (t80) REVERT: D 135 LEU cc_start: 0.9464 (tp) cc_final: 0.9046 (pp) REVERT: D 309 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9148 (tp30) REVERT: D 334 LEU cc_start: 0.9600 (mt) cc_final: 0.9374 (pp) REVERT: D 336 GLU cc_start: 0.9582 (tp30) cc_final: 0.9273 (tm-30) REVERT: E 37 MET cc_start: 0.8787 (ttt) cc_final: 0.8327 (ppp) REVERT: E 56 GLN cc_start: 0.7889 (tp40) cc_final: 0.7500 (tp-100) REVERT: E 109 PHE cc_start: 0.9177 (t80) cc_final: 0.8673 (t80) REVERT: E 113 LEU cc_start: 0.9567 (tp) cc_final: 0.9328 (tp) REVERT: E 134 HIS cc_start: 0.9046 (t70) cc_final: 0.8798 (t70) REVERT: E 334 LEU cc_start: 0.9595 (mt) cc_final: 0.9356 (pp) REVERT: E 336 GLU cc_start: 0.9561 (tp30) cc_final: 0.9261 (tm-30) REVERT: E 346 CYS cc_start: 0.9587 (OUTLIER) cc_final: 0.9360 (p) REVERT: F 37 MET cc_start: 0.8756 (ttt) cc_final: 0.8332 (ppp) REVERT: F 56 GLN cc_start: 0.7883 (tp40) cc_final: 0.7509 (tp-100) REVERT: F 135 LEU cc_start: 0.9488 (tp) cc_final: 0.9051 (pp) REVERT: F 146 LEU cc_start: 0.9741 (mt) cc_final: 0.9364 (pp) REVERT: F 267 ILE cc_start: 0.9521 (mm) cc_final: 0.9273 (mm) REVERT: F 309 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9120 (tp30) REVERT: F 334 LEU cc_start: 0.9568 (mt) cc_final: 0.9319 (pp) REVERT: F 336 GLU cc_start: 0.9581 (tp30) cc_final: 0.9277 (tm-30) REVERT: G 37 MET cc_start: 0.8771 (ttt) cc_final: 0.8359 (ppp) REVERT: G 56 GLN cc_start: 0.7842 (tp40) cc_final: 0.7501 (tp-100) REVERT: G 63 GLN cc_start: 0.8596 (mp10) cc_final: 0.8297 (mp10) REVERT: G 109 PHE cc_start: 0.9233 (t80) cc_final: 0.9018 (t80) REVERT: G 334 LEU cc_start: 0.9607 (mt) cc_final: 0.9376 (pp) REVERT: G 336 GLU cc_start: 0.9551 (tp30) cc_final: 0.9241 (tm-30) REVERT: G 363 MET cc_start: 0.7588 (pmm) cc_final: 0.7196 (pmm) outliers start: 89 outliers final: 64 residues processed: 442 average time/residue: 0.1325 time to fit residues: 89.5814 Evaluate side-chains 432 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 366 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 155 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 164 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 181 optimal weight: 0.0370 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 134 HIS C 318 HIS D 134 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 318 HIS G 134 HIS G 318 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.075588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058864 restraints weight = 71219.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060727 restraints weight = 42889.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062010 restraints weight = 29729.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062882 restraints weight = 22850.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063491 restraints weight = 18816.607| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17458 Z= 0.118 Angle : 0.706 15.462 23688 Z= 0.331 Chirality : 0.042 0.288 2814 Planarity : 0.003 0.023 2828 Dihedral : 4.453 16.571 2247 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 20.53 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 2072 helix: 1.27 (0.14), residues: 1442 sheet: -0.78 (0.61), residues: 70 loop : 0.05 (0.32), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 152 TYR 0.018 0.001 TYR A 121 PHE 0.014 0.001 PHE A 314 TRP 0.003 0.001 TRP C 85 HIS 0.009 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00245 (17444) covalent geometry : angle 0.70564 (23660) SS BOND : bond 0.00059 ( 14) SS BOND : angle 0.61662 ( 28) hydrogen bonds : bond 0.03409 ( 1113) hydrogen bonds : angle 4.33413 ( 3087) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 418 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8677 (ttt) cc_final: 0.8302 (ppp) REVERT: A 56 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7593 (tp-100) REVERT: A 63 GLN cc_start: 0.8693 (mp10) cc_final: 0.8427 (mp10) REVERT: A 109 PHE cc_start: 0.9110 (t80) cc_final: 0.8870 (t80) REVERT: A 135 LEU cc_start: 0.9389 (tp) cc_final: 0.9008 (pp) REVERT: A 309 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9156 (tp30) REVERT: A 334 LEU cc_start: 0.9642 (mt) cc_final: 0.9407 (pp) REVERT: A 336 GLU cc_start: 0.9537 (tp30) cc_final: 0.9250 (tm-30) REVERT: B 35 ASP cc_start: 0.8972 (m-30) cc_final: 0.8680 (t70) REVERT: B 37 MET cc_start: 0.8724 (ttt) cc_final: 0.8317 (ppp) REVERT: B 56 GLN cc_start: 0.7925 (tp40) cc_final: 0.7626 (tp-100) REVERT: B 109 PHE cc_start: 0.9093 (t80) cc_final: 0.8404 (t80) REVERT: B 135 LEU cc_start: 0.9434 (tp) cc_final: 0.9012 (pp) REVERT: B 143 MET cc_start: 0.9234 (ptt) cc_final: 0.8884 (ptt) REVERT: B 146 LEU cc_start: 0.9730 (mt) cc_final: 0.9369 (pp) REVERT: B 309 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9134 (mt-10) REVERT: B 334 LEU cc_start: 0.9597 (mt) cc_final: 0.9347 (pp) REVERT: B 336 GLU cc_start: 0.9575 (tp30) cc_final: 0.9274 (tm-30) REVERT: B 363 MET cc_start: 0.7336 (pmm) cc_final: 0.7034 (pmm) REVERT: C 37 MET cc_start: 0.8772 (ttt) cc_final: 0.8370 (ppp) REVERT: C 56 GLN cc_start: 0.7743 (tp40) cc_final: 0.7537 (tp-100) REVERT: C 109 PHE cc_start: 0.9083 (t80) cc_final: 0.8575 (t80) REVERT: C 128 ARG cc_start: 0.8825 (ttp-110) cc_final: 0.7886 (ptp-170) REVERT: C 146 LEU cc_start: 0.9726 (mt) cc_final: 0.9334 (pp) REVERT: C 334 LEU cc_start: 0.9599 (mt) cc_final: 0.9365 (pp) REVERT: C 336 GLU cc_start: 0.9527 (tp30) cc_final: 0.9236 (tm-30) REVERT: C 363 MET cc_start: 0.7761 (pmm) cc_final: 0.7460 (pmm) REVERT: D 37 MET cc_start: 0.8833 (ttt) cc_final: 0.8472 (ppp) REVERT: D 56 GLN cc_start: 0.7835 (tp40) cc_final: 0.7560 (tp-100) REVERT: D 109 PHE cc_start: 0.9087 (t80) cc_final: 0.8653 (t80) REVERT: D 135 LEU cc_start: 0.9402 (tp) cc_final: 0.8947 (pp) REVERT: D 309 GLU cc_start: 0.9373 (tm-30) cc_final: 0.9125 (mt-10) REVERT: D 334 LEU cc_start: 0.9598 (mt) cc_final: 0.9350 (pp) REVERT: D 336 GLU cc_start: 0.9553 (tp30) cc_final: 0.9253 (tm-30) REVERT: E 37 MET cc_start: 0.8742 (ttt) cc_final: 0.8317 (ppp) REVERT: E 56 GLN cc_start: 0.7930 (tp40) cc_final: 0.7577 (tp-100) REVERT: E 109 PHE cc_start: 0.9055 (t80) cc_final: 0.8526 (t80) REVERT: E 134 HIS cc_start: 0.8976 (t70) cc_final: 0.8750 (t-170) REVERT: E 146 LEU cc_start: 0.9745 (mt) cc_final: 0.9364 (pp) REVERT: E 152 ARG cc_start: 0.8896 (mmp80) cc_final: 0.8691 (mmp80) REVERT: E 334 LEU cc_start: 0.9583 (mt) cc_final: 0.9297 (pp) REVERT: E 336 GLU cc_start: 0.9545 (tp30) cc_final: 0.9239 (tm-30) REVERT: E 346 CYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9158 (p) REVERT: E 347 LEU cc_start: 0.9734 (mt) cc_final: 0.9465 (mt) REVERT: F 37 MET cc_start: 0.8780 (ttt) cc_final: 0.8373 (ppp) REVERT: F 56 GLN cc_start: 0.7815 (tp40) cc_final: 0.7505 (tp-100) REVERT: F 109 PHE cc_start: 0.9019 (t80) cc_final: 0.8750 (t80) REVERT: F 143 MET cc_start: 0.9260 (ptt) cc_final: 0.8939 (ptt) REVERT: F 146 LEU cc_start: 0.9739 (mt) cc_final: 0.9385 (pp) REVERT: F 308 TYR cc_start: 0.8521 (m-80) cc_final: 0.8292 (m-80) REVERT: F 309 GLU cc_start: 0.9299 (tm-30) cc_final: 0.9011 (tp30) REVERT: F 334 LEU cc_start: 0.9557 (mt) cc_final: 0.9282 (pp) REVERT: F 336 GLU cc_start: 0.9564 (tp30) cc_final: 0.9267 (tm-30) REVERT: G 37 MET cc_start: 0.8822 (ttt) cc_final: 0.8383 (ppp) REVERT: G 56 GLN cc_start: 0.7815 (tp40) cc_final: 0.7492 (tp-100) REVERT: G 63 GLN cc_start: 0.8513 (mp10) cc_final: 0.8301 (mp10) REVERT: G 109 PHE cc_start: 0.9100 (t80) cc_final: 0.8850 (t80) REVERT: G 139 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9545 (mt) REVERT: G 146 LEU cc_start: 0.9708 (mt) cc_final: 0.9308 (pp) REVERT: G 334 LEU cc_start: 0.9605 (mt) cc_final: 0.9331 (pp) REVERT: G 336 GLU cc_start: 0.9537 (tp30) cc_final: 0.9234 (tm-30) REVERT: G 363 MET cc_start: 0.7639 (pmm) cc_final: 0.7246 (pmm) outliers start: 57 outliers final: 36 residues processed: 454 average time/residue: 0.1250 time to fit residues: 87.6245 Evaluate side-chains 423 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 385 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 346 CYS Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 137 optimal weight: 0.0470 chunk 117 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 2.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 134 HIS B 318 HIS C 134 HIS C 318 HIS D 134 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 318 HIS G 134 HIS G 318 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.058113 restraints weight = 73509.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059967 restraints weight = 44346.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061230 restraints weight = 30793.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.062078 restraints weight = 23766.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.062681 restraints weight = 19678.862| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17458 Z= 0.128 Angle : 0.709 13.807 23688 Z= 0.335 Chirality : 0.043 0.338 2814 Planarity : 0.003 0.023 2828 Dihedral : 4.433 17.184 2247 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.61 % Allowed : 20.53 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 2072 helix: 1.27 (0.14), residues: 1442 sheet: -0.79 (0.61), residues: 70 loop : 0.07 (0.31), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 152 TYR 0.020 0.001 TYR D 308 PHE 0.024 0.001 PHE A 314 TRP 0.003 0.001 TRP D 74 HIS 0.008 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00282 (17444) covalent geometry : angle 0.70889 (23660) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.69498 ( 28) hydrogen bonds : bond 0.03334 ( 1113) hydrogen bonds : angle 4.37519 ( 3087) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 410 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8699 (ttt) cc_final: 0.8348 (ppp) REVERT: A 56 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7653 (tp-100) REVERT: A 63 GLN cc_start: 0.8662 (mp10) cc_final: 0.8401 (mp10) REVERT: A 109 PHE cc_start: 0.9168 (t80) cc_final: 0.8929 (t80) REVERT: A 135 LEU cc_start: 0.9419 (tp) cc_final: 0.9068 (pp) REVERT: A 143 MET cc_start: 0.9343 (ptt) cc_final: 0.8792 (ppp) REVERT: A 309 GLU cc_start: 0.9531 (tm-30) cc_final: 0.9166 (tp30) REVERT: A 334 LEU cc_start: 0.9645 (mt) cc_final: 0.9411 (pp) REVERT: A 336 GLU cc_start: 0.9544 (tp30) cc_final: 0.9250 (tm-30) REVERT: B 35 ASP cc_start: 0.9002 (m-30) cc_final: 0.8711 (t70) REVERT: B 37 MET cc_start: 0.8727 (ttt) cc_final: 0.8349 (ppp) REVERT: B 56 GLN cc_start: 0.7893 (tp40) cc_final: 0.7623 (tp-100) REVERT: B 109 PHE cc_start: 0.9182 (t80) cc_final: 0.8541 (t80) REVERT: B 135 LEU cc_start: 0.9456 (tp) cc_final: 0.9083 (pp) REVERT: B 143 MET cc_start: 0.9230 (ptt) cc_final: 0.8889 (ptt) REVERT: B 146 LEU cc_start: 0.9743 (mt) cc_final: 0.9404 (pp) REVERT: B 309 GLU cc_start: 0.9312 (tm-30) cc_final: 0.9073 (tp30) REVERT: B 334 LEU cc_start: 0.9592 (mt) cc_final: 0.9360 (pp) REVERT: B 336 GLU cc_start: 0.9583 (tp30) cc_final: 0.9277 (tm-30) REVERT: B 363 MET cc_start: 0.7335 (pmm) cc_final: 0.7026 (pmm) REVERT: C 37 MET cc_start: 0.8747 (ttt) cc_final: 0.8350 (ppp) REVERT: C 109 PHE cc_start: 0.9118 (t80) cc_final: 0.8477 (t80) REVERT: C 128 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.7877 (ptp-170) REVERT: C 143 MET cc_start: 0.9220 (ptt) cc_final: 0.8936 (ptt) REVERT: C 146 LEU cc_start: 0.9739 (mt) cc_final: 0.9353 (pp) REVERT: C 318 HIS cc_start: 0.8393 (m170) cc_final: 0.7397 (m-70) REVERT: C 334 LEU cc_start: 0.9611 (mt) cc_final: 0.9382 (pp) REVERT: C 336 GLU cc_start: 0.9560 (tp30) cc_final: 0.9254 (tm-30) REVERT: C 363 MET cc_start: 0.7724 (pmm) cc_final: 0.7429 (pmm) REVERT: D 37 MET cc_start: 0.8860 (ttt) cc_final: 0.8484 (ppp) REVERT: D 54 PHE cc_start: 0.9012 (m-80) cc_final: 0.8351 (t80) REVERT: D 56 GLN cc_start: 0.7861 (tp40) cc_final: 0.7635 (tp-100) REVERT: D 109 PHE cc_start: 0.9157 (t80) cc_final: 0.8904 (t80) REVERT: D 135 LEU cc_start: 0.9420 (tp) cc_final: 0.9062 (pp) REVERT: D 143 MET cc_start: 0.9306 (ptt) cc_final: 0.8796 (ppp) REVERT: D 309 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9120 (tp30) REVERT: D 334 LEU cc_start: 0.9589 (mt) cc_final: 0.9369 (pp) REVERT: D 336 GLU cc_start: 0.9564 (tp30) cc_final: 0.9252 (tm-30) REVERT: E 37 MET cc_start: 0.8730 (ttt) cc_final: 0.8319 (ppp) REVERT: E 56 GLN cc_start: 0.7836 (tp40) cc_final: 0.7067 (tp40) REVERT: E 109 PHE cc_start: 0.9139 (t80) cc_final: 0.8597 (t80) REVERT: E 134 HIS cc_start: 0.8963 (t70) cc_final: 0.8744 (t-170) REVERT: E 146 LEU cc_start: 0.9751 (mt) cc_final: 0.9474 (pp) REVERT: E 152 ARG cc_start: 0.8957 (mmp80) cc_final: 0.8692 (mmp80) REVERT: E 334 LEU cc_start: 0.9563 (mt) cc_final: 0.9327 (pp) REVERT: E 336 GLU cc_start: 0.9549 (tp30) cc_final: 0.9243 (tm-30) REVERT: E 346 CYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9207 (p) REVERT: E 347 LEU cc_start: 0.9755 (mt) cc_final: 0.9501 (mt) REVERT: F 37 MET cc_start: 0.8750 (ttt) cc_final: 0.8331 (ppp) REVERT: F 56 GLN cc_start: 0.7804 (tp40) cc_final: 0.7572 (tp-100) REVERT: F 309 GLU cc_start: 0.9353 (tm-30) cc_final: 0.9141 (tp30) REVERT: F 334 LEU cc_start: 0.9538 (mt) cc_final: 0.9320 (pp) REVERT: F 336 GLU cc_start: 0.9567 (tp30) cc_final: 0.9242 (tm-30) REVERT: G 37 MET cc_start: 0.8777 (ttt) cc_final: 0.8355 (ppp) REVERT: G 56 GLN cc_start: 0.7870 (tp40) cc_final: 0.7597 (tp-100) REVERT: G 63 GLN cc_start: 0.8501 (mp10) cc_final: 0.8281 (mp10) REVERT: G 109 PHE cc_start: 0.9154 (t80) cc_final: 0.8899 (t80) REVERT: G 139 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9552 (mt) REVERT: G 146 LEU cc_start: 0.9721 (mt) cc_final: 0.9335 (pp) REVERT: G 334 LEU cc_start: 0.9611 (mt) cc_final: 0.9344 (pp) REVERT: G 336 GLU cc_start: 0.9566 (tp30) cc_final: 0.9255 (tm-30) REVERT: G 363 MET cc_start: 0.7618 (pmm) cc_final: 0.7227 (pmm) outliers start: 70 outliers final: 53 residues processed: 446 average time/residue: 0.1330 time to fit residues: 90.5462 Evaluate side-chains 444 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 389 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 51 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 182 optimal weight: 0.3980 chunk 167 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 134 HIS C 134 HIS D 134 HIS D 318 HIS F 134 HIS F 318 HIS G 134 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060568 restraints weight = 72511.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062459 restraints weight = 43323.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063815 restraints weight = 29758.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064730 restraints weight = 22627.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065378 restraints weight = 18529.657| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17458 Z= 0.121 Angle : 0.733 13.050 23688 Z= 0.342 Chirality : 0.042 0.319 2814 Planarity : 0.003 0.023 2828 Dihedral : 4.321 16.542 2247 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.22 % Allowed : 22.33 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.19), residues: 2072 helix: 1.40 (0.14), residues: 1414 sheet: -0.77 (0.61), residues: 70 loop : 0.59 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 152 TYR 0.025 0.001 TYR D 308 PHE 0.019 0.001 PHE A 314 TRP 0.005 0.001 TRP C 127 HIS 0.008 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00259 (17444) covalent geometry : angle 0.73295 (23660) SS BOND : bond 0.00074 ( 14) SS BOND : angle 0.47832 ( 28) hydrogen bonds : bond 0.03296 ( 1113) hydrogen bonds : angle 4.29035 ( 3087) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 410 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8671 (ttt) cc_final: 0.8399 (ppp) REVERT: A 56 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7687 (tp-100) REVERT: A 63 GLN cc_start: 0.8583 (mp10) cc_final: 0.8329 (mp10) REVERT: A 143 MET cc_start: 0.9303 (ptt) cc_final: 0.8779 (ppp) REVERT: A 309 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9124 (tp30) REVERT: A 334 LEU cc_start: 0.9634 (mt) cc_final: 0.9396 (pp) REVERT: A 336 GLU cc_start: 0.9536 (tp30) cc_final: 0.9241 (tm-30) REVERT: B 35 ASP cc_start: 0.8995 (m-30) cc_final: 0.8644 (t70) REVERT: B 37 MET cc_start: 0.8695 (ttt) cc_final: 0.8356 (ppp) REVERT: B 109 PHE cc_start: 0.9095 (t80) cc_final: 0.8332 (t80) REVERT: B 135 LEU cc_start: 0.9436 (tp) cc_final: 0.9044 (pp) REVERT: B 143 MET cc_start: 0.9160 (ptt) cc_final: 0.8831 (ptt) REVERT: B 146 LEU cc_start: 0.9749 (mt) cc_final: 0.9402 (pp) REVERT: B 334 LEU cc_start: 0.9580 (mt) cc_final: 0.9357 (pp) REVERT: B 336 GLU cc_start: 0.9570 (tp30) cc_final: 0.9257 (tm-30) REVERT: C 37 MET cc_start: 0.8684 (ttt) cc_final: 0.8379 (ppp) REVERT: C 56 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7750 (tm-30) REVERT: C 109 PHE cc_start: 0.9035 (t80) cc_final: 0.8298 (t80) REVERT: C 128 ARG cc_start: 0.8806 (ttp-110) cc_final: 0.7892 (ptp-170) REVERT: C 143 MET cc_start: 0.9202 (ptt) cc_final: 0.8905 (ptt) REVERT: C 146 LEU cc_start: 0.9749 (mt) cc_final: 0.9360 (pp) REVERT: C 152 ARG cc_start: 0.8823 (mmp80) cc_final: 0.8612 (mmp80) REVERT: C 334 LEU cc_start: 0.9614 (mt) cc_final: 0.9384 (pp) REVERT: C 336 GLU cc_start: 0.9540 (tp30) cc_final: 0.9243 (tm-30) REVERT: C 363 MET cc_start: 0.7741 (pmm) cc_final: 0.7429 (pmm) REVERT: D 37 MET cc_start: 0.8842 (ttt) cc_final: 0.8454 (ppp) REVERT: D 109 PHE cc_start: 0.9073 (t80) cc_final: 0.8794 (t80) REVERT: D 135 LEU cc_start: 0.9424 (tp) cc_final: 0.9046 (pp) REVERT: D 143 MET cc_start: 0.9295 (ptt) cc_final: 0.8796 (ppp) REVERT: D 334 LEU cc_start: 0.9588 (mt) cc_final: 0.9368 (pp) REVERT: D 336 GLU cc_start: 0.9549 (tp30) cc_final: 0.9242 (tm-30) REVERT: E 37 MET cc_start: 0.8663 (ttt) cc_final: 0.8303 (ppp) REVERT: E 56 GLN cc_start: 0.7854 (tp40) cc_final: 0.7624 (tp-100) REVERT: E 109 PHE cc_start: 0.9081 (t80) cc_final: 0.8593 (t80) REVERT: E 134 HIS cc_start: 0.8919 (t70) cc_final: 0.8706 (t-170) REVERT: E 146 LEU cc_start: 0.9733 (mt) cc_final: 0.9450 (pp) REVERT: E 334 LEU cc_start: 0.9579 (mt) cc_final: 0.9339 (pp) REVERT: E 336 GLU cc_start: 0.9546 (tp30) cc_final: 0.9234 (tm-30) REVERT: E 346 CYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9236 (p) REVERT: E 347 LEU cc_start: 0.9751 (mt) cc_final: 0.9513 (mt) REVERT: F 37 MET cc_start: 0.8720 (ttt) cc_final: 0.8352 (ppp) REVERT: F 143 MET cc_start: 0.9197 (ptt) cc_final: 0.8407 (ppp) REVERT: F 146 LEU cc_start: 0.9752 (mt) cc_final: 0.9370 (pp) REVERT: F 152 ARG cc_start: 0.8822 (mmp80) cc_final: 0.8618 (mmp80) REVERT: F 309 GLU cc_start: 0.9374 (tm-30) cc_final: 0.9083 (tp30) REVERT: F 334 LEU cc_start: 0.9564 (mt) cc_final: 0.9343 (pp) REVERT: F 336 GLU cc_start: 0.9550 (tp30) cc_final: 0.9216 (tm-30) REVERT: G 37 MET cc_start: 0.8778 (ttt) cc_final: 0.8395 (ppp) REVERT: G 56 GLN cc_start: 0.7873 (tp40) cc_final: 0.7645 (tp-100) REVERT: G 63 GLN cc_start: 0.8437 (mp10) cc_final: 0.8220 (mp10) REVERT: G 139 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9536 (mt) REVERT: G 146 LEU cc_start: 0.9737 (mt) cc_final: 0.9350 (pp) REVERT: G 152 ARG cc_start: 0.8857 (mmp80) cc_final: 0.8633 (mmp80) REVERT: G 309 GLU cc_start: 0.9326 (tm-30) cc_final: 0.9029 (tp30) REVERT: G 334 LEU cc_start: 0.9603 (mt) cc_final: 0.9335 (pp) REVERT: G 336 GLU cc_start: 0.9530 (tp30) cc_final: 0.9225 (tm-30) REVERT: G 363 MET cc_start: 0.7693 (pmm) cc_final: 0.7310 (pmm) outliers start: 43 outliers final: 33 residues processed: 437 average time/residue: 0.1335 time to fit residues: 89.1094 Evaluate side-chains 422 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 387 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 90 optimal weight: 9.9990 chunk 7 optimal weight: 0.2980 chunk 188 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 207 HIS B 134 HIS C 134 HIS D 134 HIS D 318 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS F 134 HIS F 318 HIS G 134 HIS G 318 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.076301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059292 restraints weight = 73010.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061133 restraints weight = 43352.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062482 restraints weight = 29966.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063403 restraints weight = 22776.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064022 restraints weight = 18587.464| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17458 Z= 0.134 Angle : 0.724 12.762 23688 Z= 0.344 Chirality : 0.043 0.293 2814 Planarity : 0.003 0.023 2828 Dihedral : 4.314 17.194 2247 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.42 % Allowed : 23.05 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 2072 helix: 1.36 (0.14), residues: 1442 sheet: -0.83 (0.62), residues: 70 loop : 0.83 (0.31), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 152 TYR 0.023 0.001 TYR D 308 PHE 0.013 0.001 PHE A 314 TRP 0.003 0.001 TRP B 74 HIS 0.006 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00300 (17444) covalent geometry : angle 0.72416 (23660) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.58077 ( 28) hydrogen bonds : bond 0.03292 ( 1113) hydrogen bonds : angle 4.34025 ( 3087) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 407 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8657 (ttt) cc_final: 0.8385 (ppp) REVERT: A 63 GLN cc_start: 0.8609 (mp10) cc_final: 0.8352 (mp10) REVERT: A 143 MET cc_start: 0.9234 (ptt) cc_final: 0.8778 (ppp) REVERT: A 334 LEU cc_start: 0.9635 (mt) cc_final: 0.9400 (pp) REVERT: A 336 GLU cc_start: 0.9573 (tp30) cc_final: 0.9258 (tm-30) REVERT: B 35 ASP cc_start: 0.8983 (m-30) cc_final: 0.8632 (t70) REVERT: B 37 MET cc_start: 0.8676 (ttt) cc_final: 0.8350 (ppp) REVERT: B 109 PHE cc_start: 0.9206 (t80) cc_final: 0.8543 (t80) REVERT: B 135 LEU cc_start: 0.9467 (tp) cc_final: 0.9110 (pp) REVERT: B 143 MET cc_start: 0.9167 (ptt) cc_final: 0.8834 (ptt) REVERT: B 146 LEU cc_start: 0.9752 (mt) cc_final: 0.9403 (pp) REVERT: B 334 LEU cc_start: 0.9595 (mt) cc_final: 0.9374 (pp) REVERT: B 336 GLU cc_start: 0.9576 (tp30) cc_final: 0.9263 (tm-30) REVERT: C 37 MET cc_start: 0.8674 (ttt) cc_final: 0.8363 (ppp) REVERT: C 109 PHE cc_start: 0.9121 (t80) cc_final: 0.8419 (t80) REVERT: C 143 MET cc_start: 0.9204 (ptt) cc_final: 0.8904 (ptt) REVERT: C 146 LEU cc_start: 0.9736 (mt) cc_final: 0.9368 (pp) REVERT: C 152 ARG cc_start: 0.8846 (mmp80) cc_final: 0.8644 (mmp80) REVERT: C 334 LEU cc_start: 0.9620 (mt) cc_final: 0.9396 (pp) REVERT: C 336 GLU cc_start: 0.9571 (tp30) cc_final: 0.9263 (tm-30) REVERT: C 363 MET cc_start: 0.7766 (pmm) cc_final: 0.7461 (pmm) REVERT: D 37 MET cc_start: 0.8870 (ttt) cc_final: 0.8482 (ppp) REVERT: D 143 MET cc_start: 0.9289 (ptt) cc_final: 0.8800 (ppp) REVERT: D 309 GLU cc_start: 0.9350 (tm-30) cc_final: 0.9069 (tp30) REVERT: D 334 LEU cc_start: 0.9595 (mt) cc_final: 0.9376 (pp) REVERT: D 336 GLU cc_start: 0.9549 (tp30) cc_final: 0.9250 (tm-30) REVERT: E 37 MET cc_start: 0.8667 (ttt) cc_final: 0.8299 (ppp) REVERT: E 56 GLN cc_start: 0.7937 (tp40) cc_final: 0.7710 (tp-100) REVERT: E 109 PHE cc_start: 0.9180 (t80) cc_final: 0.8624 (t80) REVERT: E 134 HIS cc_start: 0.8913 (t70) cc_final: 0.8699 (t-170) REVERT: E 146 LEU cc_start: 0.9750 (mt) cc_final: 0.9471 (pp) REVERT: E 334 LEU cc_start: 0.9577 (mt) cc_final: 0.9351 (pp) REVERT: E 336 GLU cc_start: 0.9548 (tp30) cc_final: 0.9251 (tm-30) REVERT: E 346 CYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9221 (p) REVERT: E 347 LEU cc_start: 0.9758 (mt) cc_final: 0.9513 (mt) REVERT: F 37 MET cc_start: 0.8700 (ttt) cc_final: 0.8328 (ppp) REVERT: F 143 MET cc_start: 0.9195 (ptt) cc_final: 0.8408 (ppp) REVERT: F 146 LEU cc_start: 0.9748 (mt) cc_final: 0.9369 (pp) REVERT: F 309 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9084 (tp30) REVERT: F 334 LEU cc_start: 0.9561 (mt) cc_final: 0.9330 (pp) REVERT: F 336 GLU cc_start: 0.9555 (tp30) cc_final: 0.9216 (tm-30) REVERT: G 37 MET cc_start: 0.8801 (ttt) cc_final: 0.8438 (ppp) REVERT: G 56 GLN cc_start: 0.7932 (tp40) cc_final: 0.7724 (tp-100) REVERT: G 63 GLN cc_start: 0.8438 (mp10) cc_final: 0.8207 (mp10) REVERT: G 146 LEU cc_start: 0.9720 (mt) cc_final: 0.9374 (pp) REVERT: G 152 ARG cc_start: 0.8907 (mmp80) cc_final: 0.8703 (mmp80) REVERT: G 334 LEU cc_start: 0.9616 (mt) cc_final: 0.9354 (pp) REVERT: G 336 GLU cc_start: 0.9554 (tp30) cc_final: 0.9236 (tm-30) REVERT: G 352 ASN cc_start: 0.9265 (m110) cc_final: 0.8977 (p0) REVERT: G 363 MET cc_start: 0.7748 (pmm) cc_final: 0.7374 (pmm) outliers start: 47 outliers final: 39 residues processed: 433 average time/residue: 0.1313 time to fit residues: 87.1300 Evaluate side-chains 433 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 393 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 300 GLN A 318 HIS B 134 HIS B 318 HIS C 134 HIS D 100 ASN D 134 HIS D 318 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS F 134 HIS F 318 HIS G 134 HIS G 318 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.074268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.057203 restraints weight = 74143.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.058987 restraints weight = 44158.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060260 restraints weight = 30824.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061154 restraints weight = 23528.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061718 restraints weight = 19293.526| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17458 Z= 0.178 Angle : 0.762 12.369 23688 Z= 0.367 Chirality : 0.043 0.264 2814 Planarity : 0.003 0.023 2828 Dihedral : 4.500 19.094 2247 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.42 % Allowed : 23.62 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2072 helix: 1.25 (0.14), residues: 1414 sheet: -1.13 (0.63), residues: 70 loop : 0.66 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 152 TYR 0.022 0.001 TYR D 308 PHE 0.022 0.001 PHE C 319 TRP 0.006 0.001 TRP A 127 HIS 0.007 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00398 (17444) covalent geometry : angle 0.76160 (23660) SS BOND : bond 0.00307 ( 14) SS BOND : angle 0.80859 ( 28) hydrogen bonds : bond 0.03487 ( 1113) hydrogen bonds : angle 4.50968 ( 3087) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 402 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8679 (ttt) cc_final: 0.8399 (ppp) REVERT: A 143 MET cc_start: 0.9279 (ptt) cc_final: 0.8813 (ppp) REVERT: A 334 LEU cc_start: 0.9646 (mt) cc_final: 0.9422 (pp) REVERT: A 336 GLU cc_start: 0.9594 (tp30) cc_final: 0.9282 (tm-30) REVERT: B 35 ASP cc_start: 0.8987 (m-30) cc_final: 0.8624 (t70) REVERT: B 37 MET cc_start: 0.8708 (ttt) cc_final: 0.8368 (ppp) REVERT: B 109 PHE cc_start: 0.9269 (t80) cc_final: 0.8782 (t80) REVERT: B 135 LEU cc_start: 0.9505 (tp) cc_final: 0.9168 (pp) REVERT: B 334 LEU cc_start: 0.9598 (mt) cc_final: 0.9369 (pp) REVERT: B 336 GLU cc_start: 0.9597 (tp30) cc_final: 0.9266 (tm-30) REVERT: C 37 MET cc_start: 0.8708 (ttt) cc_final: 0.8400 (ppp) REVERT: C 109 PHE cc_start: 0.9204 (t80) cc_final: 0.8658 (t80) REVERT: C 128 ARG cc_start: 0.8890 (ttp-110) cc_final: 0.8109 (ptp-170) REVERT: C 143 MET cc_start: 0.9215 (ptt) cc_final: 0.8893 (ptt) REVERT: C 146 LEU cc_start: 0.9741 (mt) cc_final: 0.9382 (pp) REVERT: C 152 ARG cc_start: 0.8866 (mmp80) cc_final: 0.8663 (mmp80) REVERT: C 336 GLU cc_start: 0.9583 (tp30) cc_final: 0.9260 (tm-30) REVERT: C 363 MET cc_start: 0.7710 (pmm) cc_final: 0.7394 (pmm) REVERT: D 37 MET cc_start: 0.8913 (ttt) cc_final: 0.8536 (ppp) REVERT: D 109 PHE cc_start: 0.9231 (t80) cc_final: 0.9023 (t80) REVERT: D 143 MET cc_start: 0.9309 (ptt) cc_final: 0.8739 (ppp) REVERT: D 336 GLU cc_start: 0.9590 (tp30) cc_final: 0.9272 (tm-30) REVERT: D 363 MET cc_start: 0.7638 (pmm) cc_final: 0.7307 (pmm) REVERT: E 37 MET cc_start: 0.8741 (ttt) cc_final: 0.8366 (ppp) REVERT: E 56 GLN cc_start: 0.8011 (tp40) cc_final: 0.7761 (tp-100) REVERT: E 109 PHE cc_start: 0.9269 (t80) cc_final: 0.8857 (t80) REVERT: E 134 HIS cc_start: 0.8950 (t70) cc_final: 0.8599 (t-170) REVERT: E 334 LEU cc_start: 0.9595 (mt) cc_final: 0.9360 (pp) REVERT: E 336 GLU cc_start: 0.9593 (tp30) cc_final: 0.9277 (tm-30) REVERT: E 346 CYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9267 (p) REVERT: E 347 LEU cc_start: 0.9764 (mt) cc_final: 0.9526 (mt) REVERT: F 37 MET cc_start: 0.8734 (ttt) cc_final: 0.8361 (ppp) REVERT: F 143 MET cc_start: 0.9227 (ptt) cc_final: 0.8606 (ppp) REVERT: F 334 LEU cc_start: 0.9574 (mt) cc_final: 0.9347 (pp) REVERT: F 336 GLU cc_start: 0.9579 (tp30) cc_final: 0.9258 (tm-30) REVERT: G 37 MET cc_start: 0.8807 (ttt) cc_final: 0.8416 (ppp) REVERT: G 56 GLN cc_start: 0.8097 (tp40) cc_final: 0.7879 (tp-100) REVERT: G 63 GLN cc_start: 0.8505 (mp10) cc_final: 0.8106 (mp10) REVERT: G 146 LEU cc_start: 0.9743 (mt) cc_final: 0.9425 (pp) REVERT: G 152 ARG cc_start: 0.8956 (mmp80) cc_final: 0.8753 (mmp80) REVERT: G 318 HIS cc_start: 0.8272 (m170) cc_final: 0.7789 (m-70) REVERT: G 334 LEU cc_start: 0.9588 (mt) cc_final: 0.9376 (pp) REVERT: G 336 GLU cc_start: 0.9588 (tp30) cc_final: 0.9275 (tm-30) REVERT: G 363 MET cc_start: 0.7699 (pmm) cc_final: 0.7311 (pmm) outliers start: 47 outliers final: 36 residues processed: 422 average time/residue: 0.1274 time to fit residues: 83.0763 Evaluate side-chains 427 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 390 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 346 CYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 79 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 0.0070 chunk 198 optimal weight: 7.9990 chunk 37 optimal weight: 0.0030 chunk 205 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 overall best weight: 0.8610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 318 HIS B 134 HIS B 318 HIS C 134 HIS D 134 HIS D 318 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 318 HIS G 134 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.077854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060667 restraints weight = 74211.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062530 restraints weight = 44306.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.063845 restraints weight = 30595.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064773 restraints weight = 23367.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065414 restraints weight = 19165.081| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17458 Z= 0.128 Angle : 0.788 12.143 23688 Z= 0.366 Chirality : 0.043 0.349 2814 Planarity : 0.003 0.033 2828 Dihedral : 4.323 19.432 2247 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 25.79 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2072 helix: 1.20 (0.14), residues: 1484 sheet: -1.05 (0.63), residues: 70 loop : 0.77 (0.31), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 152 TYR 0.023 0.001 TYR D 308 PHE 0.022 0.001 PHE C 319 TRP 0.003 0.001 TRP C 127 HIS 0.007 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00277 (17444) covalent geometry : angle 0.78865 (23660) SS BOND : bond 0.00050 ( 14) SS BOND : angle 0.50266 ( 28) hydrogen bonds : bond 0.03301 ( 1113) hydrogen bonds : angle 4.33193 ( 3087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.07 seconds wall clock time: 55 minutes 9.56 seconds (3309.56 seconds total)